Thanks for the interest, Scott. The projects you see at the top-level of our CVS server are actually module aliases to the real folders under the org.eclipse.jsdt area. Aliases are often used to help isolate developers from restructuring of contents in the repository, as happened when we went from the WST+JST projects to what we have now. WTP may be the only top-level project that still does this, though, as it gets out of hand as more and more plug-ins, features, and test projects are added. And as you saw, the compiler breakages were the result of new plug-ins that hadn't yet been added to the project set file, which should be a rare occurrence. The Debug support is rapidly evolving, though, so I wouldn't rule out further changes between now and when 3.3 ships in June.

The PDE target you've listed is correct, but unless you plan to tinker with the org.eclipse.wst.jsdt.web.* plug-ins, you really only need the Eclipse SDK itself in your target. I don't tend to develop with that restricted a target myself, but it's an option.

The org.eclipse.jsdt/development/org.eclipse.wst.jsdt.unittests folder on the CVS server is a workspace project that can be used to run all of our unit tests in one go; it includes a shared launch configuration that should appear in your drop-down once checked out. It's a meager number of tests at the moment, as large amounts haven't been ported from the JDT test suites and remain disabled. We're slowly adding and/or re-enabling suites as we go.